Abstract: The k-ω-γ transition model is used to analyze the typical flow characteristics and boundary layer instability characteristics of a new aircraft configuration. The results indicate that the existence of cross flow is the main factor affecting large area transition of the aircraft. As the height increases, the Reynolds number decreases, and the transition onsets of windward and leeward move downstream. As the angle of attack increases, the spanwise pressure gradient on the leeward side near the head increases, the cross-flow effect is enhanced, and the transition onset moves upstream. At the same time, the head shock wave is enhanced, and the density on the windward side behind the wave increases significantly, and the Reynolds number at the outer edge of the boundary layer increases, which leads to an earlier transition on the windward side. At 0° angle of attack, the flow separation induced by the compression surface leads to an early transition near the centerline of the leeward surface, resulting in a "convex" transition profile. At 5° angle of attack, the flow separation occurs after the transition, and the "convex" transition profile disappears.